Hormonal and nutritional factors regulate the metabolism of long-chain polyunsaturated fatty acids (LC-PUFA). We aimed to determine whether ovarian hormones influence the capacity of rats to synthesize the end-products 22:6n-3 (DHA) and 22:5n-6 (n-6DPA) from their respective dietary precursors (18:3n-3 and 18:2n-6), and can regulate PUFA conversion enzymes gene transcription in brain and/or liver. Females born with a low DHA status were fed from weaning to 8 weeks of age a diet providing both essential precursors, and were concurrently submitted to sham-operated control (SOC) or ovariectomy (OVX) in combination with or without 17 beta-estradiol (E2) dosed at 8 or 16 mu g/day. Relative to SOC. OVX increased the hepatic Delta 9-, Delta 6- and Delta 5-desaturase transcripts and cognate transcription factors (PPAR alpha, PPAR gamma, RXR alpha RAR alpha), but it did not affect LC-PUFA contents in phospholipids. In comparison with SOC and OVX groups, both E2 doses prevented the increase of transcripts, while paradoxically augmenting DHA and n-6DPA in liver phospholipids. Thus, in the liver of rats undergoing ovariectomy, changes of LC-PUFA synthesizing enzyme transcripts and of LC-PUFA proportions were not correlated. In brain, ovariectomy did not modify the transcripts of lipid metabolism genes, but it decreased DHA (-15%) and n-6DPA (-28%). In comparison with SOC and OVX groups, ovariectomized females treated with E2 preserved their status of both LC-PUFA in brain and had increased transcripts of E2 receptor beta, PPAR delta, RAR alpha and LC-PUFA synthesizing enzymes. In conclusion, E2 sustained the transcription of lipid metabolism genes and proportions of neo-formed DHA and n-6DPA differently in brain and liver. (C) 2011 Elsevier Inc. All rights reserved.